.TH g_enemat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_enemat - extracts an energy matrix from an energy file

.B VERSION 4.5
.SH SYNOPSIS
\f3g_enemat\fP
.BI "\-f" " ener.edr "
.BI "\-groups" " groups.dat "
.BI "\-eref" " eref.dat "
.BI "\-emat" " emat.xpm "
.BI "\-etot" " energy.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]sum" ""
.BI "\-skip" " int "
.BI "\-[no]mean" ""
.BI "\-nlevels" " int "
.BI "\-max" " real "
.BI "\-min" " real "
.BI "\-[no]coul" ""
.BI "\-[no]coulr" ""
.BI "\-[no]coul14" ""
.BI "\-[no]lj" ""
.BI "\-[no]lj" ""
.BI "\-[no]lj14" ""
.BI "\-[no]bhamsr" ""
.BI "\-[no]bhamlr" ""
.BI "\-[no]free" ""
.BI "\-temp" " real "
.SH DESCRIPTION
\&g_enemat extracts an energy matrix from the energy file (\fB \-f\fR).
\&With \fB \-groups\fR a file must be supplied with on each
\&line a group of atoms to be used. For these groups matrix of
\&interaction energies will be extracted from the energy file
\&by looking for energy groups with names corresponding to pairs
\&of groups of atoms. E.g. if your \fB \-groups\fR file contains:

\&\fB 2\fR

\&\fB Protein\fR

\&\fB SOL\fR

\&then energy groups with names like 'Coul\-SR:Protein\-SOL' and 
\&'LJ:Protein\-SOL' are expected in the energy file (although
\&\fB g_enemat\fR is most useful if many groups are analyzed
\&simultaneously). Matrices for different energy types are written
\&out separately, as controlled by the
\&\fB \-[no]coul\fR, \fB \-[no]coulr\fR, \fB \-[no]coul14\fR, 
\&\fB \-[no]lj\fR, \fB \-[no]lj14\fR, 
\&\fB \-[no]bham\fR and \fB \-[no]free\fR options.
\&Finally, the total interaction energy energy per group can be 
\&calculated (\fB \-etot\fR).


\&An approximation of the free energy can be calculated using:
\&E(free) = E0 + kT log( exp((E\-E0)/kT) ), where ''
\&stands for time\-average. A file with reference free energies
\&can be supplied to calculate the free energy difference
\&with some reference state. Group names (e.g. residue names)
\&in the reference file should correspond to the group names
\&as used in the \fB \-groups\fR file, but a appended number
\&(e.g. residue number) in the \fB \-groups\fR will be ignored
\&in the comparison.
.SH FILES
.BI "\-f" " ener.edr" 
.B Input, Opt.
 Energy file 

.BI "\-groups" " groups.dat" 
.B Input
 Generic data file 

.BI "\-eref" " eref.dat" 
.B Input, Opt.
 Generic data file 

.BI "\-emat" " emat.xpm" 
.B Output
 X PixMap compatible matrix file 

.BI "\-etot" " energy.xvg" 
.B Output
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]sum"  "no    "
 Sum the energy terms selected rather than display them all

.BI "\-skip"  " int" " 0" 
 Skip number of frames between data points

.BI "\-[no]mean"  "yes   "
 with \-groups extracts matrix of mean energies instead of matrix for each timestep

.BI "\-nlevels"  " int" " 20" 
 number of levels for matrix colors

.BI "\-max"  " real" " 1e+20 " 
 max value for energies

.BI "\-min"  " real" " \-1e+20" 
 min value for energies

.BI "\-[no]coul"  "yes   "
 extract Coulomb SR energies

.BI "\-[no]coulr"  "no    "
 extract Coulomb LR energies

.BI "\-[no]coul14"  "no    "
 extract Coulomb 1\-4 energies

.BI "\-[no]lj"  "yes   "
 extract Lennard\-Jones SR energies

.BI "\-[no]lj"  "no    "
 extract Lennard\-Jones LR energies

.BI "\-[no]lj14"  "no    "
 extract Lennard\-Jones 1\-4 energies

.BI "\-[no]bhamsr"  "no    "
 extract Buckingham SR energies

.BI "\-[no]bhamlr"  "no    "
 extract Buckingham LR energies

.BI "\-[no]free"  "yes   "
 calculate free energy

.BI "\-temp"  " real" " 300   " 
 reference temperature for free energy calculation

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
